* Make sort_order private in SamBuilder to avoid changes/inconsistency

  with header
* Update poetry environment for newer python
* Insist sort_order is a SamOrder, elminate None option
* Allow writing with unknown sort order

fgpyo/sam/builder.py

@@ -106,7 +106,7 @@ def __init__(
  rg: Optional[Dict[str, str]] = None,
  extra_header: Optional[Dict[str, Any]] = None,
  seed: int = 42,
- sort_order: Optional[SamOrder] = SamOrder.Coordinate,
+ sort_order: SamOrder = SamOrder.Coordinate,
  ) -> None:
  """Initializes a new SamBuilder for generating alignment records and SAM/BAM files.
 
@@ -119,21 +119,17 @@ def __init__(
  extra_header: a dictionary of extra values to add to the header, None otherwise. See
  `::class::~pysam.AlignmentHeader` for more details.
  seed: a seed value for random number/string generation
- sort_order: optional sort order, if `None` reads will be output in the same order as
- they were appended.
+ sort_order: Order to sort records when writing to file, or output of to_sorted_list()
  """
 
  self.r1_len: int = r1_len if r1_len is not None else self.DEFAULT_R1_LENGTH
  self.r2_len: int = r2_len if r2_len is not None else self.DEFAULT_R2_LENGTH
  self.base_quality: int = base_quality
  self.mapping_quality: int = mapping_quality
 
- sort_order = SamOrder.Unsorted if sort_order is None else sort_order
- assert sort_order in [SamOrder.Coordinate, SamOrder.QueryName, SamOrder.Unsorted], (
- "`sort_order` for `SamBuilder` must be one of `Coordinate` `QueryName` or `Unsorted`."
- + f" Found {sort_order}"
- )
- self.sort_order: SamOrder = sort_order
+ if not isinstance(sort_order, SamOrder):
+ raise ValueError(f"sort_order must be a SamOrder, got {type(sort_order)}")
+ self._sort_order = sort_order
 
  self._header: Dict[str, Any] = {
  "HD": {"VN": "1.5", "SO": sort_order.value},
@@ -580,7 +576,7 @@ def to_path(
 
  with NamedTemporaryFile(suffix=".bam", delete=True) as fp:
  file_handle: IO
- if self.sort_order is SamOrder.Unsorted:
+ if self._sort_order in {SamOrder.Unsorted, SamOrder.Unknown}:
  file_handle = path.open("w")
  else:
  file_handle = fp.file
@@ -592,18 +588,17 @@ def to_path(
  if pred(rec):
  writer.write(rec)
 
- default_samtools_opt_list = ["-o", str(path), fp.name]
+ samtools_sort_args = ["-o", str(path), fp.name]
 
  file_handle.close()
- if self.sort_order == SamOrder.QueryName:
+ if self._sort_order == SamOrder.QueryName:
  # Ignore type hints for now until we have wrappers to use here.
- pysam.sort(*(["-n"] + default_samtools_opt_list)) # type: ignore
- elif self.sort_order == SamOrder.Coordinate:
+ pysam.sort("-n", *samtools_sort_args) # type: ignore
+ elif self._sort_order == SamOrder.Coordinate:
  # Ignore type hints for now until we have wrappers to use here.
- pysam.sort(*default_samtools_opt_list) # type: ignore
  if index:
- # Ignore type hints for now until we have wrappers to use here.
-  pysam.index(str(path)) # type: ignore
+ samtools_sort_args.insert(0, "--write-index")
+ pysam.sort(*samtools_sort_args) # type: ignore
 
  return path
 

fgpyo/sam/tests/test_builder.py

@@ -272,9 +272,9 @@ def make_sort_order_builder(tmp_path: Path, sort_order: SamOrder) -> Path:
  (SamOrder.Coordinate, ["test2", "test3", "test4", "test1"]),
  (SamOrder.QueryName, ["test1", "test2", "test3", "test4"]),
  (SamOrder.Unsorted, ["test3", "test2", "test1", "test4"]),
- (None, ["test3", "test2", "test1", "test4"]),
+ (SamOrder.Unknown, ["test3", "test2", "test1", "test4"]),
  ],
- ids=["Coordinate sorting", "Query name sorting", "Unsorted output", "Unsorted output - None"],
+ ids=["Coordinate sorting", "Query name sorting", "Unsorted output", "Unknown sorting"],
 )
 def test_sort_types(
  tmp_path: Path, sort_order: Optional[SamOrder], expected_name_order: List[str]

pyproject.toml

@@ -37,9 +37,13 @@ pysam = ">=0.22.0"
 docs = ["sphinx", "sphinx_rtd_theme"]
 
 [tool.poetry.dev-dependencies]
+setuptools = ">=68.0.0"
 pytest = ">=5.4.2"
 mypy = ">=0.770"
-flake8 = ">=3.8.1"
+flake8 = [
+ { version = ">=3.8.1", python = "<3.12.0" },
+ { version = ">=6.1.0", python = ">=3.12.0" },
+]
 black = ">=19.10b0"
 pytest-cov = ">=2.8.1"
 isort = ">=5.10.1"